Computer generates comparative gene maps

ITHACA, N.Y. -- Comparing the genomes of two related species of a plant or animal often helps to locate important genes that have been identified in one species but not in another, and can provide clues about how both species evolved from a common ancestor. But making these "comparative gene maps" has been a slow, painstaking process, something biologists do by hand over weeks, months or years, using data painstakingly collected in "wet labs" and analyzed with software designed to interpret only one map at a time.

Now, Cornell University researchers have come up with a way to do the comparison step in a few hours on a computer. In early tests, a computer-generated comparison of the genomes of rice and maize (corn) closely matched a similar map made by hand, and even suggested some relationships that had not shown up in the handmade map.

Debra Goldberg, Cornell graduate student in applied mathematics, developed the new method in collaboration with Susan McCouch, Cornell professor of plant breeding, and Jon Kleinberg, Cornell assistant professor of computer science. Goldberg described their work at the Gene Order Dynamics, Comparative Maps and Multigene Families (DCAF) workshop held September in Sainte-Adèle, Quebec, and will present a later version at the Plant and Animal Genome IX conference in San Diego in January. Their paper, "Algorithms for Constructing Comparative Maps," appears in Comparative Genomics (David Sankoff and Joseph H. Nadeau, Eds., Kluwer Academic Publishers, 2000). A software implementation of the new method soon will be available to geneticists.

"The point of this isn't just to compare rice and corn, but to be able to do it with any two species," Goldberg says. "Ideally we'd like to be able to find new evolutionary pathways."

Every so often, as reproductive cells divide, genes and segments of chromosomes get shuffled around. One chromosome meets another and pieces of DNA are moved or swapped. If those particular c

Contact: Bill Steele
Cornell University News Service

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